Book of Abstracts: Albany 2003

Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

Na+ and Rb+ Bind to the Same Sites in the Minor Groove of B-DNA

Several studies by X-ray crystallography, NMR and molecular simulations have suggested that monovalent counterions can penetrate deeply into the minor groove of B-DNA AT-tracts. However, the extent, and in some cases even the existence, of such binding remains controversial. We have recently addressed this issue by 23Na magnetic relaxation dispersion (MRD) (1). That study unambiguously identified Na+ ions in long-lived (>> 1 ns) association with several B-DNA dodecamers. Since counterions at the DNA surface are expected to be highly mobile, groove binding was implicated. This was confirmed more directly by demonstrating that the extent of long-lived Na+ binding correlates with the length of the AT-tract and that it is virtually abolished on addition of the AT-tract specific minor-groove binding drug netropsin (1). Competitive ion binding was also studied, albeit at a single frequency, and indicated that K+, Rb+, Cs+ bind with similar or slightly higher affinity than Na+ (1).

Here, we report the result of a second MRD study of ion binding to the minor groove of the [d(CGCGAATTCGCG)]2 duplex, extending the previous MRD study in important ways. First, DNA of very high purity (97% by HPLC) was used at a fivefold lower concentration (1.5 mM duplex). Second, the longitudinal and transverse relaxation dispersion profiles were recorded for both 23Na+ and 87Rb+ in the same mixed-salt (0.2 M NaCl, 0.5 M RbCl) sample before and after addition of netropsin. The new results clearly confirm low-affinity binding of Na+ to the minor groove AT-tract. Moreover, they show directly that Rb+ and Na+ ions compete for the same binding sites in the minor groove AT-tract.